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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/markitdown commit 9a16f709057f0b9f1710920cd9c7fe622b5d6373
author bgruening
date Mon, 08 Dec 2025 18:42:56 +0000
parents c7467d9d0b2b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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c7467d9d0b2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/markitdown commit 1df47411ce8651c1d4f68cd032b2afe7d5a721de
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1 <tool id="markitdown" name="Markitdown" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Convert documents to Markdown</description>
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3 <macros>
1
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4 <token name="@TOOL_VERSION@">0.1.4</token>
0
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@PROFILE@">23.0</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="3.12">python</requirement>
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10 <requirement type="package" version="@TOOL_VERSION@">markitdown</requirement>
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11 </requirements>
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12
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13 <command detect_errors="exit_code"><![CDATA[
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14 #set ext_map = {
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15 'pdf': 'pdf', 'docx': 'docx', 'pptx': 'pptx', 'xlsx': 'xlsx',
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16 'html': 'html', 'txt': 'txt', 'ipynb': 'ipynb',
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17 'markdown': 'md', 'zip': 'zip', 'tabular': 'csv', 'csv': 'csv'
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18 }
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19
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20 #set file_ext = ext_map.get($input.ext, '')
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21 #set final_ext = $ext_hint if $ext_hint else $file_ext
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22
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23 markitdown
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24 ${input}
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25 -x $final_ext
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26 #if $mime_type:
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27 -m $mime_opt
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28 #end if
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29 #if $charset:
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30 -c "$charset_opt"
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31 #end if
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32 $keep_data_uris
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33 -o '$output'
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34 ]]></command>
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35
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36 <inputs>
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37 <param name="input" type="data" format="pdf,docx,pptx,xlsx,html,txt,ipynb,markdown,zip,tabular"
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38 label="Input file"/>
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39 <param name="ext_hint" type="text" optional="true" label="Extension override"/>
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40 <param name="mime_type" type="text" optional="true" label="MIME type hint"/>
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41 <param name="charset" type="text" optional="true" label="Character set (e.g. UTF-8)"/>
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42 <param name="keep_data_uris" type="boolean" truevalue="--keep-data-uris" falsevalue="" label="Keep embedded data URIs"/>
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43 </inputs>
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44
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45 <outputs>
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46 <data name="output" format="markdown" label="Converted Markdown output"/>
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47 </outputs>
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48
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49 <tests>
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50 <test>
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51 <param name="input" value="EAR.pdf" ftype="pdf"/>
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52 <output name="output">
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53 <assert_contents>
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54 <has_text text="Tags: ERGA-BGE"/>
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55 <has_text text="Lineage: mammalia_odb10"/>
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56 </assert_contents>
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57 </output>
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58 </test>
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59
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60 <test>
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61 <param name="input" value="example.docx" ftype="docx"/>
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62 <output name="output">
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63 <assert_contents>
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64 <has_text text="# Lorem ipsum dolor sit amet, consectetur adipiscing elit."/>
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65 </assert_contents>
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66 </output>
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67 </test>
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68
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69 <!--test>
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70 <param name="input" value="example.odt"/>
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71 <param name="ext_hint" value="odt"/>
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72 <output name="output">
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73 <assert_contents>
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74 <has_text text="This is a Word document"/>
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75 </assert_contents>
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76 </output>
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77 </test-->
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78
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79 <test>
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80 <param name="input" value="report_4.html" ftype="html"/>
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81 <param name="keep_data_uris" value="true"/>
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82 <output name="output">
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83 <assert_contents>
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84 <has_text text="is the contig length such that using longer or equal length contigs produces"/>
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85 </assert_contents>
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86 </output>
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87 </test>
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88
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89 <test>
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90 <param name="input" value="example.txt" ftype="txt"/>
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91 <param name="ext_hint" value="txt"/>
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92 <output name="output">
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93 <assert_contents>
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94 <has_text text="This is a plain text file"/>
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95 </assert_contents>
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96 </output>
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97 </test>
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98
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99 <test>
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100 <param name="input" value="example.ipynb" ftype="ipynb"/>
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101 <output name="output">
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102 <assert_contents>
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103 <has_text text="print(&quot;Hello, world!&quot;)"/>
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104 </assert_contents>
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105 </output>
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106 </test>
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107 </tests>
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108
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109 <help format="markdown"><![CDATA[
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110
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111 **Markitdown** converts rich document formats (PDF, DOCX, HTML, etc.) to Markdown.
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112
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113 ---
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114
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115 ### Supported Formats:
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116
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117 - PDF, DOCX, PPTX, XLSX
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118 - HTML, TXT, Markdown
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119 - Jupyter Notebooks (IPYNB)
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120 - ZIP containing supported formats
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121 - Tabular (CSV)
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122
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123 ---
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124
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125 ### Options:
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126
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127 - **Extension override** (`-x`): hint for file type if not obvious
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128 - **MIME type** (`-m`): manual MIME hint
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129 - **Charset** (`-c`): text encoding hint
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130 - **Keep data URIs**: retain base64-encoded images
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131
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132 Project: https://github.com/microsoft/markitdown
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133 ]]></help>
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134
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135 <citations>
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136 <citation type="bibtex">
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137 @misc{markitdown2024,
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138 author = {Microsoft},
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139 title = {markitdown: Convert documents to markdown},
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140 year = {2024},
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141 howpublished = {\url{https://github.com/microsoft/markitdown}}
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142 }
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143 </citation>
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144 </citations>
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145 </tool>